Medical analysis system

ABSTRACT

The present invention relates to effective diagnosis of patients and assisting clinicians in treatment planning. In particular, invention provides a medical analysis system that enables refinement of molecular classification. The system provides a molecular profiling solution that will allow improved diagnosis, prognosis, response prediction to provide the right chemotherapy, and follow-up to monitor for cancer recurrence.

CROSS REFERENCE TO RELATED APPLICATIONS

-   -   This application claims the benefit of U.S. provisional        application Ser. No. 61/052,462 filed May 12, 2008, which is        incorporated herein by reference.

TECHNICAL FIELD OF THE INVENTION

The present invention relates to a medical analysis system. Inparticular the present invention relates to a corresponding process anda corresponding computer program product.

BACKGROUND OF THE INVENTION

Breast cancer is a complex genetic disease driven by the accumulation ofmultiple molecular alterations. Recent molecular advances inhigh-throughput genomic, transcriptomic and epigenomic technologies havemade it possible to focus on the molecular complexity of breast cancerand help guide cancer prognostication and therapy prediction.

Perou et al. demonstrated that breast cancer can be classified intodistinct groups based on their gene expression profiles. The EstrogenReceptor positive (ER+) group is characterized by higher expression of apanel of genes that are typically expressed by breast luminal epithelialcells (‘luminal’ cancer). The ER− branch covered three subgroups oftumors: 1) overexpressing ERBB2 (HER2); 2) expressing genescharacteristic of breast basal cells (basal-like cancer); and 3)normal-like samples. The clinical importance is that ER+ tumorstypically show good prognosis and basal-like and HER2 tumors have poorprognosis.

Gene expression profiling has also led to the development of twogene-expression assays, Oncotype DX and MammaPrint, which determine therisk of breast cancer recurrence in patients for early stagenode-negative breast cancer. Oncotype DX analyzes the expression of 21genes and calculates a recurrence score to identify the likelihood ofcancer recurrence in patients and an assessment of their likely benefitfrom chemotherapy. MammaPrint analyzes the expression of 70 genes andallows patients (<61 years) with early-stage breast cancer to becategorized as having a high or low risk of distant metastasis.High-risk patients may then be managed with more aggressive therapy.

Many other molecular profiling technologies are used to address similarclinical questions. Representational Oligonucleotide Microarray Analysis(ROMA) detects genomic amplifications and deletions and has enableddetection of certain copy number variation patterns and measures theircorrelation to patient survival.

Following a cancer diagnosis such as breast cancer and primary treatmentof localized cancer, a doctor has many options for therapy. How can the‘right’ decision for treatment be made? Traditionally, diagnosticimaging has played a critical role in cancer treatment choice bycharacterizing the location, morphology and spread of the tumor. Canceris correlated with changes within the DNA and its regulatory potential,and the specific characteristics of the patient's tumor cell molecularprofile can direct a clinician to the ‘right’ therapy.

Today, molecular tests categorize patients based on single-gene testslike the aforementioned ER, PR and HER2 gene expression. However, thereis still significant variation in treatment response within tumors withsimilar clinical classification and scope for improved tests using DNAmethylation and gene expression. DNA methylation affects gene regulationwithout change in the genetic code. Abnormal DNA methylation profilesare associated with diseases like cancer. Gene expression profilingassess gene activity at the level of a whole genome.

Several small startups and big companies operate in the area ofmolecular therapy planning, such as Agendia (MammaPrint™ is a prognostictest) and Genomic Health (Oncotype Dx). The target area of thesecompanies is patient stratification for chemotherapy for subsets ofbreast cancer patients (such as patients who have lymph node negative,ER positive tumors). In addition there is Adjuvant!, which focuses onproviding decision support and therapy planning services using clinicalfactors such as age, tumor size, node status, grade.

Further refinement in molecular classification however, can result indiffering clinical significance. Hence, there is a clinical need formolecular profiling solutions that will provide improved diagnosis,prognosis, response prediction to provide the right chemotherapy, andfollow-up to monitor for cancer recurrence.

Hence, an improved medical decision tool or system would beadvantageous, and in particular a more efficient and/or reliable systemwould be advantageous.

SUMMARY OF THE INVENTION

Accordingly, the invention preferably seeks to mitigate, alleviate oreliminate one or more of the above mentioned disadvantages singly or inany combination. In particular, it may be seen as an object of thepresent invention to provide a medical analysis system that solves theabove mentioned problems of the prior art with finding the appropriatetreatment for one or more patients in a fast and/or reliable manner.

Thus, an object of the present invention relates to effective diagnosisof patients and assisting clinicians in treatment planning. Inparticular, it is an object of the present invention to provide amedical analysis system that solves the above mentioned problems of theprior art in obtaining this and other objects.

Thus, the first aspect of the invention relates to a medical analysissystem for pre-clinical and/or clinical analysis of data obtained fromat least one patient, the system comprising:

an internal database (IDB), the database comprising a collection ofdata, analysis results, flow definitions, and tool definitions, andother related data for tools that utilize a database repository,

a database access unit (DA), the unit being adapted for providing accessto the internal database,

a flow definition unit (FD), the unit providing execution of aconfigurable flow of analysis and visualization of a plurality of datamodalities, the plurality of data modalities comprising:

a first bio-molecular modality comprising bio-molecular data related tothe patient, and

a second clinical modality comprising clinical data related to thepatient,

a tool execution engine (TEE), having an interface for the system toconfigure and instantiate one or more tools working on one or more ofthe data modalities,

a tool repository, the repository comprising a collection of tools forwhich the system is configured to execute, said tools complying with aset of rules in order for it to be possible to visualize their executionin a graphical user interface (GUI),

one or more associated external databases (EDB), the externaldatabase(s) representing data stored in the said system itself, or in adatabase different from the said internal database (IDB), and

a graphical user interface (GUI), said interface simultaneouslyvisualizing data, analysis results, and outcome of one or more toolexecutions, and wherein said interface is further adapted forsimultaneously visualizing:

-   1) an outcome of said first bio-molecular modality, and-   2) an outcome of said second clinical modality.

The invention is particularly, but not exclusively, advantageous forobtaining a multimodal approach for designing personalized therapy. Theinvention thereby facilitate a fully integrated genomic design andanalysis toolbox, which enables access to clinical information about thepatient along with pertinent molecular information (e.g. gene expressionas well as differential DNA methylation).

Furthermore, the invention facilitate integration of multiple machinelearning tools specialized in a) gene expression profiling, b) DNAmethylation profiling, c) combining clinical parameters with molecularlevel information, d) combining with clinical, biological knowledge withmolecular data, and/or d) integration of molecular modalities bystatistical tools.

The invention allows for a configurable flow of execution ofbioinformatic tools facilitating advanced means to analyze data ofmultiple modalities and to browse the data and the results from thesignature-discovery processes. It provides a lightweight interface to a(dynamic set of) new and existing tools and allows them to be executedwith little or no modification.

The advantage of this solution is rapid implementation and execution ofanalysis processes and ease of communicating methods and resultsclinicians and other interested parties.

The system according to the first aspect may be applied to at least onepatient in an in pre-clinical situation. One advantage is that the dataand the information on the patient may be used be the system to discoverbio-molecular signatures. Another advantage of doing so is that thesystem may integrate the data of the patient in system in order toexpand the data available.

The system according to the first aspect may also be applied to a groupof patients.

The system according to the first aspect may be applied to one patientin a clinical situation. Thereby the system enables the physician toidentify any bio-molecular/clinical signatures in the data of thepatient thereby assisting the diagnosis and further treatment of thepatient.

In line with the previous, the system according to the first aspect maybe function may also function as a clinical decision support system(CDS).

The system according to the first aspect also may be configured suchthat said first bio-molecular modality and said second clinical modalityis integrateable by a machine learning algorithm, the result of saidintegration being visualizable in the graphical user interface. Themajor advantage of this set up is that it enables the discovery ofcomplex bio-molecular signatures in very large and complex datacollections.

Further, the system according to the first aspect also may be configuredsuch that said first bio-molecular modality and said second clinicalmodality is integrateable by a statistical algorithm, the result of saidintegration being visualizable in the graphical user interface.

The system according to the first aspect also may be configured suchsaid that first bio-molecular modality and said second clinical modalityis integrateable based on their respective genomic annotation, theresult of said integration being visualizable in the graphical userinterface.

In a further embodiment, the system according to the first aspect may beconfigured such that said first bio-molecular modality is based on ahigh-throughput data sampling modality. The system thereby enables theanalysis of high-throughput data in a context including data of othermodalities.

The system according to the first aspect may be configured such that thesample provided by said high-throughput data sampling modality comprisedata on at least 100.000 parameter/species.

The system according to the first aspect may also be configured suchthat said first bio-molecular modality is selected from the groupconsisting of a high-throughput gene expression profiling, DNAmethylation status profiling, comparative genomic hybridizationanalysis. These modalities generate large and complex data sets whichmay be applied to the system and used to identify bio-molecularsignatures across the modalities.

In one particular version of the system according to the first aspect,said flow definition unit (FD) comprises at least one furtherbio-molecular modality. The version of the system integrates morebio-molecular modalities.

In a further version of the system according to the first aspect, saidfurther bio-molecular modality is selected from the group consisting ofa high-throughput gene expression profiling, DNA methylation statusprofiling, comparative genomic hybridization analysis, and SNP profile.

In the system according to the first aspect the patient may have aclinical condition selected from the group consisting cancer, acardiovascular disease, a metabolic disease, a gastro-intestinaldisease, a neurological disease. One advantage of this system is that isenables the use of the system to discover bio molecular and clinicalsignature associated with a specific condition and subsequentlyapplication of the system and signature in a clinical setting.

In a second aspect, the present invention relates to a process for thediscovery of bio-molecular or clinical signature associated with aspecific clinical condition comprising the use of the medical analysissystem according to the first aspect of the invention.

The invention is particularly, but not exclusively, advantageous fordiscovering of bio-molecular or clinical signature related to clinicalcondition is selected from the group consisting of cancer, acardiovascular disease, a metabolic disease, a gastro-intestinaldisease, a neurological disease.

More particular, not exclusively, advantageous the process may bediscovering of bio-molecular or clinical signature related breast canceror colon cancer. Breast cancer and colon cancer are known to correlatewith aberrant gene expression profiles/DNA methylation profiles.

Further, the process according to the second aspect may be for thediscovery of a signature selected from the group consisting of geneexpression signature, DNA methylation status signature, comparativegenomic hybridization signature and SNP signature. These modalitiestypically generates large amount of data which requires high capacitysystem to reveal any bio-molecular present.

In a third aspect, the present invention relates to a process forclinical decision support comprising the use of the medical analysissystem according to the first aspect of the invention.

The invention also provides that the data of a patient is applied to thesystem for identification of a bio-molecular or clinical signatureassociated with a clinical condition. The advantage of this embodimentis that the application of the bio-molecular/clinical signature may beused to indicate whether a patient is likely suffer from a clinicalcondition associated with said signature.

In a fourth aspect, the invention relates to a computer program productbeing adapted to enable a computer system comprising at least onecomputer having data storage means associated therewith to control ananalysis process according to the second aspect of the invention.

This aspect of the invention is particularly, but not exclusively,advantageous in that the present invention may be implemented by acomputer program product enabling a computer system to perform theoperations of the second aspect of the invention. Thus, it iscontemplated that some known medical analysis system may be changed tooperate according to the present invention by installing a computerprogram product on a computer system controlling the said medicalanalysis system. Such a computer program product may be provided on anykind of computer readable medium, e.g. magnetically or optically basedmedium, or through a computer based network, e.g. the Internet.

The first, second, third and fourth aspect of the present invention mayeach be combined with any of the other aspects. These and other aspectsof the invention will be apparent from and elucidated with reference tothe embodiments described hereinafter.

BRIEF DESCRIPTION OF THE FIGURES

The present invention will now be explained, by way of example only,with reference to the accompanying Figures, where

FIG. 1 shows the architecture of the system.

FIG. 2 shows a conceptual flow scenario for data access, analysis, andclinical decision.

FIG. 3 shows the states of the system with respect to the analysiscontext and visual presentation.

FIG. 4 shows an example of the main screen of the system of theinvention.

FIG. 5 shows an example of loading patient information from thedatabase.

FIG. 6 shows an example of a screen related to the histopathologicalmodality.

FIG. 7 shows an example of a screen related to the comparative genomichybridization (CGH) modality.

FIG. 8 shows an example of a screen related to the gene expressionmodality.

FIG. 9 shows an example of a screen related to the DNA methylationmodality

FIG. 10 shows an example of a screen related to exploration of twogroups of gene expression signatures, one using solely gene expressiondata, and another using gene expression data in conjunction with DNAmethylation data.

FIG. 11 shows an example of a feature-browser for gene expressionsignatures.

FIG. 12 shows an example of a Genecard link for gene expressionsignatures.

FIG. 13 shows an example of a screen related to exploration of the DNAmethylation signatures.

FIG. 14 shows an example of a feature-browser for DNA methylationmarkers.

FIG. 15 shows an example of a clinical decision support (CDS) screen forthe methylation Signature

FIG. 16 shows an example of a screen related to the genetic algorithmsummary tool.

FIG. 17 shows an example of a split-screen related to compression of theoutput of two genetic algorithm summary tools.

FIG. 18 shows an example of a screen related to the gene co-occurrencetool.

FIG. 19 shows an example of a screen related to the methyl binding sitestool.

FIG. 20 shows an example of a screen related to top down hierarchicalsorting (TDHS).

FIG. 21 shows an example of a screen related to the gene expressionfiltering tool.

FIG. 22 shows an example of a screen related to a multimodal correlationfeature analysis—graphics output.

FIGS. 23 and 24 shows an example of a screen related to a multimodalcorrelation feature analysis—text output.

FIG. 25 shows an example of a CDS screen for gene expression.

FIG. 26 shows four possible outputs of a Genetic Algorithm (GA)—basedtool that is designed to automatically evolve a subset of features thatbest predicts the ground truth labeling of samples.

FIG. 27 shows a comparison of the performance values of all candidatefeature subsets that were discovered and the feature subsets that werefound significant in the post-processing analysis

FIG. 28 shows an example of a feature browser for gene expressionsignatures visualizing multiple features.

FIG. 29 shows a flowchart describing the process of generating thevisualization of a gene signature meta-data.

FIG. 30 shows an example of presenting the distribution of genesignature meta-data.

FIG. 31 show an example of Top Down Hierarchical Sorting (TDHS).

FIG. 32 shows an example of the correlation of gene expression and DNAmethylation data.

The present invention will now be described in more detail in thefollowing.

DETAILED DESCRIPTION OF THE INVENTION

There is a need for translational clinical tools based on molecularbioinformatics, particularly in current cancer care. The inventorsdisclose with the present invention a tool for clinical decision makingthat relies on genomic and epigenomic measurement modalities as well asclinical parameters such as histopathological results and survivalinformation.

An object of the present invention is to facilitate discovery ofmolecular profiles of clinical conditions and enable their use in aclinical setting. The present invention describes new technologies toobtain genomic information from tissue specimen and to assist diagnosis,determination of the appropriate therapy, and follow-up.

The inventor's Physician Accessible Preclinical Analytics Application(PAPAyA) integrates a powerful set of statistical and machine learningtools that could leverage the connections among the differentmodalities. The system is easily extendable and reconfigurable tosupport integration of existing research methods and tools into powerfuldata analysis pipelines. PAPAyA enables analysis of data from clinicalstudies, formulation of new clinical hypotheses, and facilitatesclinical decision support by abstracting molecular profiles forclinicians. A current configuration of PAPAyA with examples of itsperformance on breast cancer molecular profiles is used to present thesystem in action.

The inventors present a multimodal molecular approach for designingpersonalized therapy. In particular, the method focuses on tumorsubtyping and identifies patient subpopulations that would most likelyrespond to chemotherapy (e.g. Herceptin) leading to a predictivediagnostic test.

The inventors provide a prototype of genomic design and analysis toolboxthat improves preclinical discovery of molecular profiles thatcharacterize samples of breast and ovarian cancer patient biopsies. Theinventors also provide results from a set of decision analysis toolsthat aid in patient stratification and predict therapy response.

The system of the invention provides a configurable platform thatenables analysis and interpretation of results around clinical studiesbased on high-throughput molecular measurements. The system of theinvention combines bioinformatics software methods to be used fortranslational research, pre-clinical, and parts for clinicalapplications. The system of the invention covers the following aspects:

Integrating analysis of multiple modalities to infer correlatedinformation about most important genes/loci that may contribute tooutcome and patient status (and will be used for therapy response). Theinventors provide the incorporation of patient information from geneexpression and DNA methylation in addition to clinical parameters suchas histological grade, node, ER/PR status, and outcome.

Combining various machine learning tools to analyze this data (beyonddescription of such tools in the literature)

Use of such integrated analysis for diagnosis, prognosis, therapyresponse, and follow-up.

The inventors provides results from a set of decision analysis tools tobrowse through patient information and gene signatures and individuallyanalyze gene expression profiles as well as differential DNA methylationprofiles as well as to make inferences based on correlation andco-ocurrence. These tools rely both on high-throughput gene expressionprofiling as well as other clinical predictive and prognostic indicesbased on patient information such as tumor size, hormonal andhistopathological parameters.

The inventors provide these tools and results using the Genomic Designand Analysis Toolbox (GDAT), called Papaya, that contains methods thathelp in the preclinical discovery phase for breast and ovarian cancer.Specifically, these tools include feature subset selection,classification, clustering methods and top-down hierarchical sorting aswell as decision analysis, incorporating biological knowledge aboutprotein-DNA interactions, clinical prognostic indices, DNA methylationand gene expression profiling data. We present results from GDATleveraging multiple molecular modalities, for example high-throughputgene expression profiling and DNA methylation profiling, to furtherimprove diagnostics.

The systems of the invention provide a comprehensive view by combiningdiscovered molecular signatures with imaging and additional clinicalinformation. Further, the system may be employed as an assisting tool informing diagnosis, selecting treatment direction (e.g. hormone orchemotherapy) and the appropriate monitoring the progress and follow-upof the disease. The system may also be used to provide molecularinformation packages (e.g. combined molecular signatures withcorresponding meta data) as a service to clinicians or to third-partydecision support systems. Moreover, the system may be used to developand provide molecular-medicine-enhanced clinical guidelines that can becustomized to a patient's molecular profile.

Some of the challenges with high-throughput genomic data analysis lie incoping with high measurement and biological noise, a huge number offeatures and limited patient samples. The present invention providesstatistically-rigorous approach of utilizing multiple molecularmodalities and clinical information, which is likely to eliminate manyspurious signals, so that we can focus on the underlying biology of thedisease.

Fusion of more traditional clinical predictors of outcome with molecularinformation (e.g. methylation and gene expression) from the tumorsthemselves is considered useful, but learning how to interpretprobabilistic information and communicate results with physicians andpatients is a major challenge. The solution to the problem is providedwith the present invention. The system may assist the application ofpersonalized medicine in the clinic.

There is a clear clinical need for an integrated decision support systemthat takes into account clinical, histopathological, and molecularprofiles of the patient. Such a system will provide a one-stop solutionto aid informed decision making by the tumor board (radiologist,pathologist, surgeon, radiotherapist and oncologist).

The description above is primarily of an embodiment for pre-clinical usefor clinical research. In another embodiment, this invention can besimilarly used as a clinical application.

The System

The architecture of the present system has the following components, cf.also FIG. 1A;

GUI: the Graphical User Interface combines components that showsynchronously data, analysis results, and outcome of tool executions.

DATA ACCESS (DA): Provides access to the database of study information,measurements, and analysis results.

FLOW DEFINITION (FD): Provides execution of the configurable flow ofgenomic data analysis and clinical/molecular data-browsing steps.

TOOL EXECUTION ENGINE (TEE): Provides interface for the application toseamlessly configure and instantiate tools from various platforms. Thisallows application extension with new tools to be easily added to theconfiguration and the flow with little or no modification.

INTERNAL DATABASE IDB): Collection of study data, analysis results, theflow and tool definitions, and any other data for the external toolsthat utilize a database repository.

TOOL “REPOSITORY” (TR): The collection of tools for which theapplication is configured to execute. These tools comply with the basicset of rules in order for it to be possible to visualize theirexecution.

EXTERNAL “DATABASE” (EDB): The collection of all data and other filesthat the external tools use stored somewhere on the file system or in adatabase different from the IDB.

A slightly modified architecture of the present system is illustrated inFIG. 1B, where flow definition (FD) and data access (DA) of FIG. 1A iscombined into flow control of FIG. 1B. Similarly, the general userinterface (GUI) is subdivided into modules of user interface,presentation and action as shown in FIG. 1B. The lower structure is alsoslightly modified as shown in FIG. 1B, where a database managementsystem is shown together with the modules “tools” and “external data”.

Accordingly, one aspect of the present invention relates to a medicalanalysis system for pre-clinical and/or clinical analysis of dataobtained from at least one patient, the system comprising:

an internal database (IDB), the database comprising a collection ofdata, analysis results, flow definitions, and tool definitions, andother related data for tools that utilize a database repository,

a database access unit (DA), the unit being adapted for providing accessto the internal database,

a flow definition unit (FD), the unit providing execution of aconfigurable flow of analysis and visualization of a plurality of datamodalities, the plurality of data modalities comprising:

a first bio-molecular modality comprising bio-molecular data related tothe patient, and

a second clinical modality comprising clinical data related to thepatient,

a tool execution engine (TEE), having an interface for the system toconfigure and instantiate one or more tools working on one or more ofthe data modalities,

a tool repository, the repository comprising a collection of tools forwhich the system is configured to execute, said tools complying with aset of rules in order for it to be possible to visualize their executionin a graphical user interface (GUI),

one or more associated external databases (EDB), the externaldatabase(s) representing data stored in the said system itself, or in adatabase different from the said internal database (IDB), and

a graphical user interface (GUI), said interface simultaneouslyvisualizing data, analysis results, and outcome of one or more toolexecutions, and wherein said interface is further adapted forsimultaneously visualizing:

-   1) an outcome of said first bio-molecular modality, and-   2) an outcome of said second clinical modality.

In one embodiment, the medical analysis system is applied to at leastone patient in an in pre-clinical situation. In another embodiment, themedical analysis system is applied to a group of patients. In yetanother embodiment, the medical analysis system is applied to onepatient in a clinical situation. In yet another embodiment, the medicalanalysis system is a functioning as a clinical decision support system(CDS).

In the preclinical situation the patient data may be applied to thesystem to expand the data and/or for the purpose of identifying abio-molecular or clinical signature correlating with a clinicalcondition in the context of cancer, cardiovascular diseases, metabolicdiseases, gastro-intestinal diseases, or neurological diseases.

In one embodiment of the invention, the system of the invention is as amultimodal approach for the assisting the design of a personalizedtherapy.

The system provides:

A fully integrated genomic design and analysis toolbox which enablesaccess to clinical information about the patient along with pertinentmolecular information (e.g. gene expression as well as differential DNAmethylation)

Integration of multiple machine learning tools specialized in a) geneexpression profiling b) DNA methylation profiling c) combining clinicalparameters with molecular level information d) combining with clinical,biological knowledge with molecular data d) integration of molecularmodalities by statistical tools

The invention allows for a configurable flow of execution ofbioinformatic tools facilitating advanced means to browse the data andthe results from the signature-discovery processes.

It provides a lightweight interface to a (dynamic set of) existing toolsand allows them to be executed with little or no modification.

The advantage of this solution is rapid implementation and execution ofanalysis processes and ease of communicating methods and resultsclinicians and other interested parties.

Modalities

In one embodiment of the present invention, the medical analysis systemaccording to any of the preceding claims, wherein said firstbio-molecular modality and said second clinical modality isintegrateable by a machine learning algorithm, the result of saidintegration being visualizable in the graphical user interface.

In second embodiment of the present invention, the medical analysissystem according any of the preceding claims, wherein said firstbio-molecular modality and said second clinical modality isintegrateable by a statistical algorithm, the result of said integrationbeing visualizable in the graphical user interface.

In a third embodiment of the present invention, The medical analysissystem according any of the preceding claims, wherein said firstbio-molecular modality is based on a high-throughput data samplingmodality.

High-throughput analysis in the context of the present refers to thelarge scale analysis of biological data addressing biological orclinical questions otherwise unattainable using conventional methods atthe time of filing of the present application. High-throughput isfurther defined by the modality generating the data for analysis.

High-throughput gene expression analysis typically involves the analysisof expression profiles comprising data of thousands expression productsper sample. Gene expression data from a single microarray experiment cantrace the activities of a number of genes ranging from a few thousandsto hundreds of thousands under hundreds of stimuli.

High-throughput DNA methylation status profiling (such as ahigh-throughput differential methylation hybridization (DMH) microarrayor MOMA microarray) comprising data of 100,000 s CpG sites/islands persample.

Mass-spectrometry proteomics typically involves simultaneous measurementof 100,000 s mass-charge (m/z) values of protein peptides in ameasurement setup that involves one or more mass spectrometers andadditional steps to focus one particular subset of proteins in thebiological sample.

Thus in one embodiment, high-throughput is defined at the range from100,000 s to several millions such test in a single measurement (e.g. ona microarray). Specifically, gene expression data typically measures10,000 s gene expression profiles, DNA methylation measures themethylation status of 100,000 s fragments in CpG islands,mass-spectrometry proteomics typically measures 100,000 s of m/z values.

In another embodiment, high-throughput refers to the level ofdistinction that would be applicable to all modalities would be theirproperty that enables rapid simultaneous execution of millions ofbiochemical, genetic or pharmacological tests.

In one embodiment, the sample provided by said high-throughput datasampling modality comprise data on at least 100.000 parameter/species.

The system of the present invention enables integration of a wide rangeof modalities including but not limited to high-throughput modalities.

In one embodiment the first bio-molecular modality is selected from thegroup consisting of a high-throughput gene expression profiling, DNAmethylation status profiling, comparative genomic hybridizationanalysis, mass-spectrometry proteomics, single nucleotide polymorphism(SNP) and other genome-wide sequencing modalities.

In another embodiment, the first bio-molecular modality is selected fromthe group consisting of histology modalities such as immunohistology,ELISA, enzymatic activity, PCR such as Q-PCR, RT-PCR.

In one embodiment, the second clinical modality comprising clinical datarelated to the patient relates to data such as age, gender, data fromphysical examination of the patient and other information (e.g. datafrom interview of patient) collected by the clinician.

Apart from the first bio-molecular modality the system enables theintegration of multiple bio-molecular modalities. Thus, in a furtherembodiment, the flow definition unit (FD) comprises at least one furtherbio-molecular modality.

The additional bio-molecular modality or modalities may be any of thebio-molecular modality described herein. Thus, in one embodiment, thefurther bio-molecular modality is selected from the group consisting ofa high-throughput gene expression profiling, DNA methylation statusprofiling, comparative genomic hybridization analysis, and SNP profile.

In a further embodiment, the integration of the first bio-molecularmodality and said second clinical modality is integrateable based ontheir respective genomic annotation, wherein the result of saidintegration being visualizable in the graphical user interface. Thegenomic annotation can be gene name, function, pathway information, GeneOntology.

Flow, States and Transactions in the System

A non-limiting conceptual flow scenario is provided with FIG. 2. Toimplement this system, in this embodiment 5 screen types defined:

A Patient Screen:

Purpose: Demonstrate how validation patients (samples) are matched tothe database of signatures.

Data: samples (including methylation/expression profiles, and patienthistory, clinical indices), signatures.

Tools: match with signatures, summary of relevant (matched) signatures.

Control: load patient; expand a signature; select summary of signatures(e.g. gene ranks, pathways, . . . ); Decision Support.

A Signature Screen:

Purpose: Illustrate contents and properties of a signature (optionallyin the context of a sample or a set of signatures).

Data: Signatures (set(s) of genes/loci), annotations (links to extresources, e.g. NCBI).

Tools: Match, summary of relevant (matched) signatures (summary ofstatistical data).

Control: Navigate to “analytics” or to the earlier steps in theanalysis, change view to emphasize or remove visual elements (or evenchange the view completely—e.g. from ordered list of genes, to heatmap).

A Tool1 Versus Tool2 Screen:

Purpose: Provide means to show output from 2 tools simultaneously withthe option to “drive” tool 2 from tool 1 for comparative purposes andfor multimodal data integration.

Data: Any—depends on the tools

Tools: Any tool.

Example:1) tool1=hierarchical clustering vs. tool2=top down hierarchicalsorting. Example 2) tool1 on gene exp data vs. tool1 on methylationdata.

Control: Provide parameters and drive tool 2. Navigate back to wherecalled from.

Tool Screen:

Purpose: Execute a tool within a predefined context information (e.g.current sample, current signature, current output from other tool)

Data: Any—depends on the tools

Tools: Any tool.

Control: Rudimentary parameter input. Default parameters should be usedand could be changed on the fly if necessary. Get some context of theflow and update context for subsequent tool calls. Navigate back towhere called from. Navigate to similar tools.

Navigate to tools that precede it in the pipeline.

A CDS Screen:

Purpose: Visualize one or more ideas on how may the result of a matchfor a patient sample be translated into a CDS-like output.

Data: Sata based on analysis and annotation

Tools: None. Just information presented. E.g. clinical indices, therapyplanning

Control: Some data may contain hyperlinks to external sources (e.g.PubMed publications, pathway info). Navigate back to where called from.

In one embodiment of the present invention, the flow is defined usingstates and possible transitions (actions) as in the example in FIG. 3.Each state also has a screen type associated with it. To implement theallowed transitions, in this embodiment we specify:

State from: The state originating the transition

State to: The resulting state

Description: free-text description of the action

Action type: tool-call (will call an external tool); custom (willexecute an internally-defined action); button (will call an externaltool from a button provided on the screen)

Tool: If applicable, a pointer to the description of the tool to becalled.

Existing constraint: The flag(s) that need to be set or unset byprevious actions in order for this action to be allowed.

Set constraint: The flag(s) that this action will set.

Unset constraint: The flag(s) that this action will unset.

The application starts in an initial state. Upon entering a state, theapplication queries the transition table and compiles a subset of allpossible transitions based on the state entered and the set and unsetconstraints in the system. The Flow Definition Unit uses thisspecification maintain the state of the system as the user navigatesthrough the data and the tools.

The following data structures define the flow, the tools linked to theflow and their parameters:

Flow Definition:

Field Description state_from Current state Type Tool execution; internaltransition; . . . Description Free-text description Action Tool name(previous slide); initialization; internal actions constraint_eUser-defined variables that can be set to define constraints. Forexample methylation modality active vs. expression modality active;analysis mode vs. decision support mode; etc. constraint_s constraint_ustate_to Next stateTools Definition

Field Description Tool Name of the actual tool Number of ParametersExecution Directory Platform <EXE, R, Matlab, Perl, Python> PreparePlatform Call e.g. load_data(‘file1.txt’) Function to Call result =func1(par1) Call prefix result = func1(par1) Call Result Variable e.g.result Tool Output type Text or image Tool Supports Split Mode Can showresult on half screenTools Parameters Definitions

Field Description Tool Name of the actual tool Parameter# ParameterParameter type Numeric/text/<list>/context Parameter Description Concisedescription in free text Parameters Range Optional; supports choicelists Parameter default value Default value

Below a non-exhaustive list of generic tools is provided. The tools aregrouped into four groups according to the application and functionality:

Pre-Processing:

-   i. Analysis of probe-level properties-   ii. Scaling-   iii. Normalization    Biomarker Discovery:-   i. Feature Ranking-   ii. Survival Analysis-   iii. Feature Subset Selection-   iv. Filters-   v. Wrappers    Cross-Modal Tools:-   i. Visualization of data from two or more modalities-   ii. Translation from one modality to another modality-   iii. Correlation of measured modalities and respective biomarkers    Clinical Decision Support Tools:-   i. Signatures characterization based on one or more patient sample    profiles-   ii. Visualization of one or more patient profiles across multiple    modalities-   iii. Visualization of one or more patient profiles with respect to    repertory of patient profiles.    The Application of the System

The present invention combines bioinformatics software tools to be usedfor translational research, pre-clinical, and parts for clinicalapplications.

The system allows for patient-centric analysis and informatics-assisteddiscovery to be performed in a systematic processing pipeline that couldbe fine-tuned for specific clinical questions. For example, by two usescenarios of integrated analysis of multi-modality retrospective breastcancer data.

Having selected a specific patient sample, the user is presented withthe basic patient-centric clinical data about the tumor, such as tumorsize, stage and grade, and histopathological data such as hormonereceptor status (estrogen receptor ER and progesterone receptor PR) andErbB2 amplification.

Furthermore, the Clinical Data Explorer also provides access tosignatures derived from high-throughput gene expression, DNA methylationand copy number measurements. New signatures can also be derived usingthe discovery algorithms inside PAPAyA from single or a combination ofhigh-throughput measurements. Such signatures address different clinicalneeds—benign vs. malignant, tumor subtype, and relapse free survival.

From the gene expression tab in the system, the user can access thesignatures derived from mRNA profiling. For example, in FIG. 10, ascreenshot of the system interface when browsing a list of signaturesthat classify the patient as belonging to either luminal or basalsubtype. Here, one of the candidate signatures is expanded to gainaccess to their member genes (including GIMAP6, TBCC, CRABP2 as topthree genes) with access to gene cards and feature browser. One mayexplore one of these genes with the Feature Browser tool (cf. FIGS. 11,and 28) that plots the expression values of any given gene(s) grouped byclinical parameters. The user may observe that this gene's expressionlevel also correlates with the hormone status (under expressed inhormone positive and over expressed in hormone positive) and tumor grade(over expressed in grade I and II, and under expressed in grade III).This tool thus enables the user to gain insights into clinicalassociations that were not used in the signature discovery process. Thiscan be used to establish the significance of the genes as well asconfidence in the signatures in which these genes are found.

In another use scenario, the system is used to explore molecularsignatures based on DNA methylation microarray measurements (cf. FIG.13). To assess the signatures, a different tool is used, whichvisualizes the methylation states for specific loci in the genome (cf.FIG. 14).

Accordingly one aspect of the present invention relates to a process forthe discovery of bio-molecular or clinical signature associated with aspecific clinical condition comprising the use of the medical analysissystem according to any of the preceding claims.

The data may be obtained from a patient suffering from any clinicalcondition. In one embodiment of the present invention, the patient has aclinical condition selected from the group consisting cancer, acardiovascular disease, a metabolic disease, a gastro-intestinaldisease, a neurological disease.

The bio-molecular or clinical signatures discovered by the system may beapplied to the clinic eg. for the stratification of patients in clinicalconditions.

In one embodiment, the clinical condition is selected from the groupconsisting of cancer, a cardiovascular disease, a metabolic disease, agastro-intestinal disease, a neurological disease. In a particularembodiment, the cancer is breast cancer or colon cancer.

The signature may relate to any of the modalities or combinations of anymodalities employed by the systems of the invention.

Thus, in one embodiment, the signature is a gene expression signature,DNA methylation status signature, comparative genomic hybridizationsignature and SNP signature.

In one embodiment, the system provides means of analysis complex dataobtained from molecular diagnostic and monitoring tests. These targetedtests provide a molecular view of the progress of a patient's diseaseright from the point of diagnosis, to treatment planning, to follow upof treatment.

In another embodiment, the system of the invention may be used todevelop decision support systems that aid the clinicians throughout thewhole care cycle. These systems provide a comprehensive view bycombining the discovered molecular signatures with the imaging andtreatment planning information. These systems can suggest therapychoices (e.g. hormone or chemotherapy) and the appropriate imagemodalities for monitoring the progress of the disease.

In a third embodiment, the system is used to provide molecularinformation packages (e.g. molecular signatures with associated metadata) to the clinicians or to third party decision support systems.

In yet an embodiment, the system is used to develop enhanced clinicalguidelines that can be customized to a patient's molecular profile. Suchguidelines may be useful in molecular medicine.

The inventor further provide the for use in a clinical setting in acompletely different way—therefore the inventors have provided differentways to explore and present the data thus allowing for clinical decisionsupport (CDS) to be applied to patient data. The CDS part of PAPAyAassists in the interpretation of the patient's tumor profile. Itprovides a personalized view with respect to the selected signature.

Signatures that are derived from the discovery process are eventuallyapplied to stratify the patient samples and can be used to assignconfidence in a stratification based on the signature's performance withrespect to all patients in the database. Currently the PAPAyA system'sCDS modules include Support Vector Machine based classifiers forpredicting tumor subtype using gene expression or methylation profilingdata. These statistics could provide the clinician with the insights totailor the treatment to the physiological state of the patient. Breastcancer clinical prognostic indices such as Nottingham Prognostic Indexand St. Gallen Consensus can also be easily incorporated into patientassessment. Additionally the architecture allows for integration ofthird party signatures into the system.

A further aspect of the present invention relates to a process forclinical decision support comprising the use of the medical analysissystem according to any of the preceding claims.

The process reflects the continuation of the signature discovery processinto the application of the system and the signature in a clinicalapplication.

Thus in one embodiment, the data of a patient is applied to the systemfor identification of a bio-molecular or clinical signature associatedwith a clinical condition.

It should be noted that embodiments and features described in thecontext of one of the aspects of the present invention also apply to theother aspects of the invention.

All patent and non-patent references cited in the present application,are hereby incorporated by reference in their entirety.

The invention will now be described in further details in the followingnon-limiting examples.

EXAMPLES Example 1

The application opens with the Analytics screen with a default patientloaded (FIG. 4). The user can load patient information from this screenand begin the different kinds of analyses provided in the Genomic Designand Analysis Toolbox (GDAT). The first modality that is shown isHistology, where you can see the summary of the histopathologicalanalysis performed on the patient sample.

Loading Patient Information from the Database

Summarized patient (samples) information from the database is shown andthe application allows selection (highlighting) of a patient for furtheranalysis (FIG. 5).

Example 2

The Histopathological Modality

Summary of the histo-pathological analysis for a given patient is shownin this screen including status of Estrogen Receptor, ProgesterorReceptor, Her2 overexpression by FISH and immunohistochemistry (FIG. 6).

Example 3

The CGH Modality

Summary of the Comparative Genomic Hybridization (CGH) data associatedwith the sample, such as number of gene amplifications, deletions, etc.,along with the Firestorm index for the sample from ROMA data(Representational Oligonucleotide Microarray Analysis). Cf FIG. 7.

Example 4

The Gene Expression Modality

Summary of the gene expression data for the sample, allowing furtherexploration of the gene expression signatures etc. (cf. FIG. 8).

Example 5

Summary of the differential methylation data obtained by MethylationOligonucleotide Microarray Analysis (MOMA) for the sample is shown. Thisalso allows further exploration of potential methylation-basedsignatures (cf. FIG. 9).

Example 6

Exploring the Gene Expression Signatures

This screen can be reached by clicking on the “Signatures” button at thebottom right hand corner of the Gene Expression modality screen (cf.FIG. 10). Signatures identified by using gene-expression data alone aswell as signatures discovered using gene expression and methylation dataanalysis are shown. The top signatures ranked according to theirstatistical relevance to the particular patient are shown. Clicking onany of the signatures on the left-hand side of the screen provides asummary of all the genes included in the signature. There are links toexternal sources of data for the individual genes such as“FeatureBrowser” and “Genecard”.

Example 7

The FeatureBrowser for Gene Expression Signatures

When the FeatureBrowser is called (clicked on) for a particular gene,this tool shows the distribution of the gene's expression levels acrossall the patients sorted according to different clinical annotations suchas hormone receptor (HR) status, Her2FISH status and tumor grade status(cf. FIG. 11).

Example 8

The Genecard Link for Gene Expression Signatures

Clicking on the “Genecard” link for any given gene, opens up an Internetbrowser that allows the user to get publicly-available information aboutthe gene from external resources (cf. FIG. 12).

Example 9

Exploring the Methylation Signatures

Similar to the gene expression signatures, the user can choose toexplore the DNA Methylation signatures within the Methylation modality.This also allows for further exploration of the methylation markersusing the FeatureBrowser links (cf. FIGS. 13 and 14).

The CDS Screen for the Methylation Signature

In this screen (cf. FIG. 14), the methylation signatures are used tocluster the patients, with the current patient being marked by an ‘X’mark in the figure. This allows the user to view the patient's clinicalannotation based on the patient's methylation profile.

The “Cluster Methylation” button on the left allows the user to clusterthe patients according to any of the methylation signatures, thusproviding access to many different clustering outputs similar to the oneshown here.

Example 10

The Discovery Section

The discovery section provides access to many of the discovery toolsthat were used in generating the signatures. Here we include statisticalmethods and public as well as proprietary machine learning algorithms.The individual tools can be access using the buttons on the left (cf.FIG. 16).

Example 11

The Genetic Algorithm Summary Tool

This tool displays a summary of the learning and validation performanceof the genetic algorithm-based signature discovery tool. The tool can beused to display the learning and performance on individual screens or asa split-screen, as shown in FIGS. 16 and 17.

Example 12

The Gene Co-Occurrence Tool

This tool displays the gene co-occurrence within the signaturesdiscovered by the genetic algorithm. The tool can be used to look at thegene co-occurrence for signatures that were discovered using geneexpression data alone by clicking on the “GA Gene Nwks (EXP)” button ORthe signatures discovered by exploiting both gene expression andmethylation data using the “GA Gene Nwks (EXP-MET)” button (cf. FIG.18).

Example 13

The Methyl Binding Sites Tool

This tool shows relevant methyl binding sites for the significantdifferential methylation probes (sequences), see FIG. 19.

Example 14

The Top-Down Hierarchical Sorting Tool

Top down hierarchical sorting (TDHS) is similar to a clusteringalgorithm except it performs sorting of the most similar patterns (wherelocal match is high) as opposed to hierarchical clustering where the twopatterns show global similarity (cf. FIG. 20).

Example 15

The Gene Expression Filtering Tool

This tool allows the user to filter the gene expression data based onn-fold expression intensity change (cf. FIG. 21).

Example 16

Multimodal Correlation Feature Analysis—Graphics Output

This tool shows the output of correlation between gene expression dataand differential DNA methylation data. The correlation is measured basedon patient outcome. The samples need to be positively correlated in thesurvived (positive outcome) and negatively correlated in the deceased(negative outcome) category (cf. FIG. 22). A Multimodal Feature Analysisis shown in FIGS. 23 and 24.

Example 17

Clinical Decision Support Section

The CDS Screen for Gene Expression

From the signatures screen (cf. FIG. 25), the user can select aparticular signature and then move to the Clinical Decision Support(CDS) screen that gives the particular patient's stratificationinformation using the signature that was selected.

This also provides information about the rank of the signature for thegiven patient, the probability of the stratification prediction usingthe chosen signature and also the length f the signature (number offeatures in the signature).

This screen allows the clinical expert (user) to go back to thesignatures screen or the patient data screen.

Feature Subset Selection Using a Genetic Algorithm Wrapper for a SupportVector Machines Classifier

The key stage of the gene expression data analysis is the search forfeature (gene) subsets which can on their own describe the entiredataset with respect to a particular labeling of the patient samples.The inventors are using a Genetic Algorithm (GA)—based tool that isdesigned to automatically evolve a subset of features that best predictsthe ground truth labeling of the samples. In particular, the (filtered)set of gene expression data contains 3,501 gene expression probes and104 patient samples labeled based on two breast cancer subtype groups:Luminal and Basal. The tool was run 100 times on different combinationsof 78 samples for learning and 26 samples for validation. The exact samesetup was repeated on data where the patient sample labels are alsopermuted in each of the 100 runs. This data is later used to select thestatistically-significant subsets.

Among other post-processing tasks, the inventors also estimate theoverall distribution of errors in millions subsets evaluated by ourtool. This gives us a coarse characterization of the performance of thetool and also a convenient method to compare distinct runs. Inparticular, two setups of the search tool were compared. In the firstone, we let the GA wrapper evolve feature subsets based solely on itsclassification on the 3,501×104 gene expression data. In the secondsetup, the inventors used classification information on around 60% ofthe samples from a separate analysis based on DNA methylation data. Inthis setup, the inventors combined the gene expression and DNAmethylation (mis)classification performance to provide additionalguidance in the search. The key idea is with the multi-modal approach isthat the methylation data serves as an additional (orthogonal) source ofinformation—a constraint, that will assist in the search through a vastsearch space.

FIG. 26 shows the four possible outputs in this tool. Each graph showsthe distribution of classification errors in both setups. The keyobservations are:

Both for the proper or the permuted labeling of the patients, thelearning performance is similar both with and without the addedmethylation-based constraint. This is a direct result of thecase-poor-feature-rich data (3,501 features vs. 78 samples), whichallows the tool to fit the data to pretty much any labeling.

The validation performance plots demonstrate that our tool actuallyfinds meaningful feature subsets. In the expression-only analysis, thevalidation performance (on the 26 unseen samples) is quite differentfrom the performance on the permuted labels (median of 3.5% errors vs.41.3% errors).

The validation performance in the methylation-constrained run also showsthe same distinct validation error distribution between the proper andthe permuted labels (3.2% vs. 40.8% median misclassifications), but alsoa slight validation performance improvement in the methylation-drivencase.

Example 18

Characterizing Signatures using Statistical Significance of LearningPerformance and Probability Estimates of Predicted Labels.

The GA-SVM has the ability to generate thousands of signatures withvarying degrees of performance on the learning data. While the GA itselfhas a mechanism to choose signatures that have lower learning errors andshorter lengths, the resulting output of the GA-SVM still requiresfurther characterization. In order to do this, the GA-SVM isindependently run using 100 independent permutations of the outcomelabels for the learning data. Using the output of the GA for thepermuted trials, the tool estimates the parameters of the Gumbel (type-Iextreme value) distribution using the distribution of learning errorsacross all signatures of a given size. Thus, if there are signatures ofsizes ranging from 10 through 45 in the GA run, separate EVD parametersare calculated for each one of those sizes. Using the performance of theGA in discovering good-performing signatures on random data as thebackground distribution, the inventors can now identify whether thesignatures identified by the GA on the actual data are statisticallysignificant. Furthermore, due to the large number of gene signatures,the tool adjusts for multiple comparisons, and selects only thosesignatures achieving a learning performance that was extremely unlikelyto have been found by chance in the given data (p<0.05%). Amongst thosesignatures that pass this “p-value filter”, the best performing ones aremost likely to be larger signatures. Therefore, the tool selects 100 ofthe largest signatures from the pool of subsets that survived thep-value filter.

As can be seen from FIG. 27, the selected signatures (in blue) havesignificantly better validation performance compared to all thesignatures generated by the GA-SVM tool.

Finally, the selected gene expression signatures are ranked in thecontext of every sample based on the confidence of their predicted labelfor the sample. This confidence measure is a function of the distance ofthe sample from the hyperplane defined by the signature.

Example 19

Visualizing Gene Expression Across Patients Sorted by ClinicalAnnotation

Once gene signatures that discriminate patients between multiple classesare discovered, it is critical to explore and characterize the genes toget some insight into mechanisms of disease and gain confidenceregarding their functional relevance. Breast cancer microarray geneexpression data often provides various clinical parameters for thepatient e.g. tumor grade, hormone receptor status etc. that aid theclinician in choosing an appropriate treatment plan. As an exploratorystep, it is important to assess how the particular genes in thesignature correlate with clinical annotations. For example, one canask—do the genes that discriminate between luminal and basal subtypes ofcancer—show clustering within a clinical annotation like hormonereceptor status? If the answer is yes, the hormone receptor status(which often indicates the aggressiveness of the disease) can be linkedto the particular subtypes and further hypotheses regarding mechanismscan be generated. Our Feature Browser tool enables the user to visualizethe expression intensity of a gene across patients that are sortedaccording to a particular clinical annotation.

The current version of the tool, focuses on three clinicalannotations 1) hormone receptor status 2) Her2FISH status and 3) tumorgrade (cf. FIG. 28). The inventors provide brief descriptions of each ofthese annotations. Hormone receptor status tests shows whether or notestrogen and/or progestorone hormones fuel the tumor. Cancer that ishormone-sensitive (e.g. ER+) is slightly slower growing and has a betterchance of responding to hormone-suppression treatment, than cancer thatis hormone receptor negative (e.g. ER−). Hormone-negative cancer willrespond to other kinds of treatment, and hormone-suppression may not beneeded. Her2FISH status determines overexpression of HER2 protein in thebreast cancer tissue. This epidermal growth receptor is associated withaggressive breast cancer. HER2 positive patients are good candidates forHerceptin treatment. Tumor grade is a system used to classify cancercells in terms of how abnormal they look under a microscope and howquickly the tumor is likely to grow and spread. Based on the microscopicappearance of cancer cells, pathologists commonly describe tumor gradeby four degrees of severity: Grades 1, 2, 3, and 4. The cells of Grade 1tumors resemble normal cells, and tend to grow and multiply slowly.Grade 1 tumors are generally considered the least aggressive inbehavior. On the other hand, the cells of Grade 3 or Grade 4 tumors donot look like normal cells of the same type. Grade 3 and 4 tumors tendto grow rapidly and spread faster than tumors with a lower grade.

In the gene expression signature discovery process of the presentinvention, CRABP2, (cellular retinoic acid binding protein 2) isdetermined to be a lead discriminator. In FIG. 11, the Feature Browsertool shows that the expression of this gene is clustered according tomultiple clinical annotations. Hormone receptor positive patientsgenerally have higher levels of CRABP2 expression than hormone receptornegative patients. From the visualization, one might speculate thatCRABP2 is related to the hormone receptor pathway of the disease. FIG.28 shows CRABP2 in the context of two other genes that do not appear tofollow the same pattern. A quick literature search reveals that theretinoic acid pathway is important in cancer progression.

Example 20

Tool for Visualizing the Meta-Data of a Gene Signature

The purpose of this tool is to provide visualization of the meta-dataassociated with a gene signature. Gene signatures are subsets of genesthat could be generated by statistical methods such as geneticalgorithms. Further description on the generation of the signatures isincluded in the section titled: Feature Subset Selection Using a GeneticAlgorithm Wrapper for Support Vector Machines Classifier.

An example of a meta-data source is the Gene Ontology (GO). The GeneOntology is a controlled vocabulary of terms organized as an acyclicdirected graphs. This ontology is split into three related ontologiescovering basic areas of molecular biology: the molecular function ofgene products, their role in multi-step biological processes, and theirlocalization to cellular components. Researchers worldwide annotate geneproducts, i.e., characterize gene products using terms from theontology, and submit them to the GO project to be included in geneannotation files. In a gene annotation file, each annotation is anassociation of a single gene product with a single GO term. A geneproduct can be annotated by terms indicating the cellular components itis located in, its molecular functions, and the biological processes itparticipates in.

The annotations (meta-data) of genes in a signature provide anunderstanding of the biological meaning of the signature as somemeta-data may be more abundant than others. The following paragraphdescribes the process of generating the visualization of a genesignature meta-data. A flowchart describing this process is depicted inFIG. 29.

-   1. Get the gene signature, the desired biological context, and the    display parameters. The gene signature can be an index to list of    that contain gene subsets. The user defines the biological context    to be explored. Examples of biological contexts are Cellular    Component, Molecular Function, and Biological Process. The user can    also define the presentation parameters, such as the number of items    to be presented, and the display mode of full screen or half screen.-   2. Get the meta-data associated with the gene signature. For    example, obtain the Gene Ontology annotations associated with the    genes in the signature. Furthermore, these annotations can be    limited to a biological context defined by the user.-   3. Calculate the distribution of the meta-data. For example, it    calculates the distribution of the Gene Ontology annotations that    were previously collected.-   4. Sort the distributions in descending or ascending order.-   5. Present in a visual aid (e.g. histogram) the top n distributions.    An example of this display is depicted in FIG. 30.

Example 21

Finding Methyl-Binding Protein DNA Binding Sites

The program identifies methyl binding sites in DNA sequences. The toolhas been designed to work with microarray probes and recognize specificpatterns within these probe sequences.

The inventors apply the pattern search to differentially methylatedsequences. Our CpG island array contains CpG islands genome-wide. Basedon the hybridization experiments followed by statistical analysis weobtain a set of loci (probes/sequences) which are differentiallymethylated. This enables easier biological interpretation of theresults. The inputs to the program include:

-   1. Index file—This file contains a list of indices that correspond    to the MspI fragments on which we wish to perform the analysis. The    first line of the index file is considered header information and    not processed.-   2. Microarray Probes annotation file—This file contains the probe    IDs, their sequence, and other relevant information. For the MOMA    array, the information that is processed includes:-   a. MspFrag IDs-   b. Sequence-   c. Neighboring genes and their distance to the Msp fragment. These    values are listed for both 5′ and 3′ directions and both on sense    and anti-sense strands.

The first line is considered to be the header information and is notprocessed.

The overall flow of the program is as follows:

-   1. Feed the microarray annotation file into an array.-   2. For each index in the index file, extract the corresponding row    from the annotation file array. There is a direct correspondence    between the index number specified in the index file and the row    number of the corresponding MspFragment.-   3. Split the Msp Fragment row into an array of values.-   4. Calculate the nearest gene to the MspFragment.-   5. Perform a simple regular expression match to check for the list    of methyl binding sites on the sequence of the Msp fragment    (accessed by its position in the row array).-   6. Print the hits to a file along with the nearest gene and the    minimum distance.    The program prints out a file with:-   1. The particular pattern or the methyl binding site identified-   2. The MspFragID-   3. The nearest gene to the Msp fragment (gene symbol)-   4. The distance to the nearest gene.    Sample Printout:

Kaiso: MspFrag129193 355698 KIAA0427 Kaiso: MspFrag87210 482172 BC033889Kaiso: MspFrag139352 99006 AK074590 MeCP2: MspFrag145432 293059 CEBPBKaiso: MspFrag6016 12977 MGC15668 MeCP2: MspFrag148218 1146 ZNF295MeCP2: MspFrag121388 357633 LHX1 Kaiso: MspFrag27766 1055474 GPR27MeCP2: MspFrag27766 1055474 GPR27 Kaiso: MspFrag86939 326583 LRP5 MeCP2:MspFrag86939 326583 LRP5 Kaiso: MspFrag150179 219969 BCR Kaiso:MspFrag46871 24399 HLA-F MZIF: MspFrag46871 24399 HLA-F Kaiso:MspFrag108348 22589 AK000173 MeCP2: MspFrag137260 269802 ZNF507 Kaiso:MspFrag47714 14469 BC091488 MeCP2: MspFrag1006 61125 BC065369 Kaiso:MspFrag110545 131366 AK127296 MeCP2: MspFrag128335 813522 GATA6 MeCP2:MspFrag152493 3200 CELSR1 Kaiso: MspFrag42758 341720 CXXC5 Kaiso:MspFrag144741 4395 MAFB

Example 22

Top Down Hierarchical Sorting

The method sorts the rows based on the values found in each column anddetects and groups those rows exhibiting one or more strong patterns inthe same column. With this sorting method content in distinct columns isanalyzed individually.

Since patterns are searched on individual columns and no global metricneeds to be computed across the columns, our method is well suited forparallelization, as opposed to standard clustering algorithms.

In the tool this method is applied as a sorting (clustering) approach todetect patterns in microarray experimental data. The problem withmicroarray data is that there is huge disparity of number of probes(features) vs. number of samples. By focusing on single gene (or locus)the influence of single genes on the entire classification and subsetselection problem is shown. By focusing on single data sample/patientthe inventors can detect genes similarly expressed for eachsample/patient.

In the example provided the columns represent data samples while rowsrepresent methylation levels of the genes (loci) in the microarray forthat specific data sample. Each data sample can originate from differentpatients, or from different tissue of one patient.

The Sorting Method Proceeds as Follows:

Derives histograms of the values in each column

Sorts rows based on histogram comparison for each column

Build Histograms

For each column, values that are “similar” are grouped together andhistograms showing the number of values falling in each bin are built.

Sorting

Next, for each column one or more histogram bins are selected, accordingto specific criteria (e.g. the largest bin). Based on the histogrambins, the domain is then split according to a chosen algorithm intogroups of rows (clusters) and the selection process is repeated in eachof the subdomains until a stopping criterion is reached. Based on theclusters that are generated, the same algorithm specifies the requiredpermutations on the rows (sorting).

Perform Top Down Hierarchical Sorting (TDHS)—FIG. 31.

With TDHS first the longest pattern (i.e. the one that corresponds tothe largest histogram bin) in any of the columns is computed. Thelargest histogram bin provides the largest number of rows that share a“similar” value. Once the largest value in all histograms across allcolumns (for each column there is a single histogram) is found, thecolumn of the largest histogram is selected and the rows contributing tothe longest histogram bin (i.e. longest pattern) are grouped together.Based on the longest pattern, TDHS splits the domain of rows into thosecontaining the longest pattern and the rest. The whole domain of rows issplit this way into the group sharing a similarity in that column andthe rest, obtaining two “clusters” (although this is not a clusteringalgorithm in the strict sense of the word we adopt this terminology). Inthe next iterations, histograms of the values are built again or thecomputed histograms are updated to reflect the split into clusters. Ineach of the two clusters, the (next) longest histogram bin is selectedand the domain is again split into two clusters. The iterations stopwhen the size of the longest histogram is below a predefined threshold,when the user-defined number of long patterns to be extracted wasreached, or when each of the two clusters contains a single row. In theend we will have a hierarchy of patterns. We can choose to display ateach step either both clusters or only the one with the longest pattern.This strategy may miss patterns (or parts of) when they are split in aprevious step. One variation on TDHS is to stop splitting one side ofthe tree—the one that already contains the longest pattern. This willresult in a one-sided multi-leaved binary tree.

Example 23

Correlation of Gene Expression and DNA Methylation Data (FIG. 32)

The tool uses statistical correlation between gene expression featuresand differential DNA methylation order to find genes (features) that arestrongly correlated with loci in other modality. We use a method tocorrelate features from one modality (RNA and DNA Methylation) to otherand find the features that are most highly correlated and predictive inorder to predict the outcome of an unknown case. We select the pair offeatures that correlate the best in case of one indication(benign/survived) and selection of another pair of features in case ofopposite indication (malignant/died). A regression model is generated ofthe pairs of features for prediction. Based on this regression model, wepredict an unknown case's indication. While training we use aleave-one-out method: all the patient cases but one are used fortraining and one case is used for testing.

The method is used in two possible modes based on the supplied data:

-   1. Only best performing signatures from gene expression data set vs.    Best performing signatures from differential DNA methylation    dataset.-   2. All gene expression features are correlated vs. all differential    DNA methylation loci.

Example 24

Visualizing Fragment Methylation Across Patients Sorted by Subtype

It is critical to explore and characterize the fragments that areinvolved in the disease pathology on a fragment by fragment basis to getsome insight into their functional relevance. Breast cancers havevarious clinical parameters for the patient e.g. tumor grade, hormonereceptor status etc. and the cancers can be subgrouped in differenttypes. As an exploratory step, it is important to assess how theparticular fragment in the signature correlates with these subgroups.

The current version of the tool, plots the given fragments methylationstatus in the given patient in conjunction with a set of patients chosenfrom the database. The patients are grouped according to their subgroupand the patient methylation status is highlighted in a black rectangle.

Example 25

Visualizing Cluster Dendrogram of the Patients According to HierarchicalClustering

When a signature is obtained, it is important to look how the signaturegroups patients into various subtypes. This type of visualization ispossible both for gene expression data as well as for DNA methylationdata. Then we can see if the different subgroups are relevant in aclinical setting—such as with regard to outcome, histopathology,receptor status etc.

For a given signature, we perform hierarchical clustering using Pearsoncorrelation as a distance metric. The dendrogram output is thenannotated using clinical parameters such as ER status. The given patientin the cluster is denoted by an X. Then the clinician can make adetermination if the patient is classified as being in a group with ahigh or low risk of recurrence, ER status etc. Also the dendrogram givesan idea of how the patient may belong to an atypical group. Sometimes,the clinical parameters may indicate that the patient may be responsiveto therapy and belonging to a ER positive subgroup. But in the contextof the signature, the patient may be classified as belonging to the ERnegative group with bad prognosis. Here the clinician may have to treatthis patient as possibly having a bad risk profile according to thesubgrouping even though the classical clinical parameters indicateotherwise.

In final two examples, a conceptual series of steps is described thatinclude most key innovative aspects of the presented invention. Thesystem is given high-throughput (gene expression and DNA methylation)and clinical data for 200 patients with a survival follow-up of at least10 years for all patients. The data is loaded in the internal databaseand the system is configured to use the tools described in the text ofthis invention.

Example 26

In this example, the gene expression data is analyzed using a series oftools that are available to the user as the analysis progresses.Initially, the user select one of the filtering tools and based on thisselection, the context of the analysis is set for gene expression andthe next set of available tools is for example genetic algorithm wrapperaround a classifier designed for gene expression data. The result ofthis analysis is a set of candidate signatures that the researcher cananalyze and prioritize based on the application of additional availabletools in this context. One of these tools is to re-analyze the datausing the DNA methylation measurements as an additional input to thegenetic algorithm for feature subset selection. The output of this is anadditional set of candidate signatures that the researches can againanalyze and prioritize using more tools registered with the system. Inthe end one or more if these signatures are selected of clinicalvalidation and the research portion of the PAPAyA application iscomplete. The key to this aspect of the innovation is to continuouslyprovide the user with the applicable tools in the context of theanalysis which include the selected modality and the stage in thepipeline (e.g. pre-processing, analysis, or post-processing).

Example 27

In this example, one or more candidate signatures discovered in theresearch mode of the invention have been validated and moleculardiagnostic tests are available to the clinical and are part of theclinical practice. The clinical decision support mode of the applicationallows the clinical to view the molecular profiles of the patient, butmore importantly, the system will provide based on the context access totools that allow for visualization and processing of the patient data inthe context of other clinical studies. For example, the clinical maywant to view the patient's profile in the context of the originalclinical study that determined the signature on which the diagnostictest is based. Again, the system maintains the current context of thedecision support interaction and provides the clinical with the relevanttools that allow for switch between molecular and clinical modalitiesand other relevant sources of data.

The invention can be implemented in any suitable form includinghardware, software, firmware or any combination of these. The inventionor some features of the invention can be implemented as computersoftware running on one or more data processors and/or digital signalprocessors. The elements and components of an embodiment of theinvention may be physically, functionally and logically implemented inany suitable way. Indeed, the functionality may be implemented in asingle unit, in a plurality of units or as part of other functionalunits. As such, the invention may be implemented in a single unit, ormay be physically and functionally distributed between different unitsand processors.

Although the present invention has been described in connection with thespecified embodiments, it is not intended to be limited to the specificform set forth herein. Rather, the scope of the present invention islimited only by the accompanying claims. In the claims, the term“comprising” does not exclude the presence of other elements or steps.Additionally, although individual features may be included in differentclaims, these may possibly be advantageously combined, and the inclusionin different claims does not imply that a combination of features is notfeasible and/or advantageous. In addition, singular references do notexclude a plurality. Thus, references to “a”, “an”, “first”, “second”etc. do not preclude a plurality. Furthermore, reference signs in theclaims shall not be construed as limiting the scope.

The invention claimed is:
 1. A medical analysis system for pre-clinicaland/or clinical analysis of data obtained from at least one patient, thesystem comprising: an internal database (IDB), the database comprising acollection of data, analysis results, flow definitions, and tooldefinitions, and other related data for tools that utilize a databaserepository, a database access unit (DA), the unit that provides accessto the internal database, a flow definition unit (FD), the unitproviding execution of a configurable flow of analysis and visualizationof a plurality of data modalities, the plurality of data modalitiescomprising: a first bio-molecular modality comprising bio-molecular datarelated to the patient, and a second clinical modality comprisingclinical data related to the patient, a tool execution engine (TEE),having an interface for the system to configure and instantiate one ormore tools working on one or more of the data modalities, a toolrepository, the repository comprising a collection of tools for whichthe system is configured to execute, said tools complying with a set ofrules in order for it to be possible to visualize their execution in agraphical user interface (GUI), one or more associated externaldatabases (EDB), the external database(s) representing data stored inthe said system itself, or in a database different from the saidinternal database (IDB), and a graphical user interface (GUI), saidinterface simultaneously visualizing data, analysis results, and outcomeof one or more tool executions, and wherein said interface furthersimultaneously visualizes: 1) an outcome of said first bio-molecularmodality, and 2) an outcome of said second clinical modality.
 2. Themedical analysis system according to claim 1, wherein the medicalanalysis system is applied to at least one patient in an in pre-clinicalsituation.
 3. The medical analysis system according to claim 1, whereinsaid analysis system is applied to a group of patients.
 4. The medicalanalysis system according to claim 1, wherein said analysis system isapplied to one patient in a clinical situation.
 5. The medical analysissystem according to claim 1, wherein the medical analysis system is afunctioning as a clinical decision support system (CDS).
 6. The medicalanalysis system according to claim 1, wherein said first bio-molecularmodality and said second clinical modality is integrateable by a machinelearning algorithm, the result of said integration being visualizable inthe graphical user interface.
 7. The medical analysis system accordingto claim 1, wherein said first bio-molecular modality and said secondclinical modality is integrateable by a statistical algorithm, theresult of said integration being visualizable in the graphical userinterface.
 8. The medical analysis system according to claim 1, whereinsaid first bio-molecular modality and said second clinical modality isintegrateable based on their respective genomic annotation, the resultof said integration being visualizable in the graphical user interface.9. The medical analysis system according to claim 1, wherein said firstbio-molecular modality is based on a high-throughput data samplingmodality.
 10. The medical analysis system according to claim 9, whereinthe sample provided by said high-throughput data sampling modalitycomprise data on at least 100.000 parameter/species.
 11. The medicalanalysis system according to claim 1, wherein said first bio-molecularmodality is selected from the group consisting of a high-throughput geneexpression profiling, DNA methylation status profiling, comparativegenomic hybridization analysis.
 12. The medical analysis systemaccording to claim 1, wherein said flow definition unit (FD) comprisesat least one further bio-molecular modality.
 13. The medical analysissystem according to claim 1, wherein said further bio-molecular modalityis selected from the group consisting of a high-throughput geneexpression profiling, DNA methylation status profiling, comparativegenomic hybridization analysis, and SNP profile.
 14. The medicalanalysis system according to claim 13, wherein said patient has aclinical condition selected from the group consisting cancer, acardiovascular disease, a metabolic disease, a gastro-intestinaldisease, a neurological disease.
 15. The medical analysis system ofclaim 1, wherein said system further discovers a bio-molecular orclinical signature associated with a specific clinical condition. 16.The medical analysis system according to claim 15, wherein the clinicalcondition is selected from the group consisting of cancer, acardiovascular disease, a metabolic disease, a gastro-intestinaldisease, a neurological disease.
 17. The medical analysis systemaccording to claim 16, wherein said cancer is breast cancer or coloncancer.
 18. The medical analysis system according to claim 1, whereinsaid signature is a gene expression signature, DNA methylation statussignature, comparative genomic hybridization signature and SNPsignature.
 19. A medical analysis process for pre-clinical and/orclinical analysis of data obtained from at least one patient, theprocess comprising: executing, with a flow definition unit (FD), aconfigurable flow of analysis and visualization of a plurality of datamodalities, the plurality of data modalities comprising: a firstbio-molecular modality comprising bio-molecular data related to thepatient, and a second clinical modality comprising clinical data relatedto the patient, instantiating, with a tool execution engine (TEE), oneor more tools working on one or more of the data modalities, wherein theTEE has an interface for the system to configure wherein a toolrepository comprises a collection of tools for which the system isconfigured to execute, and the tools comply with a set of rules tovisualize their execution in a graphical user interface (GUI),simultaneously visualizing, with the GUI, data, analysis results, and anoutcome of one or more tool executions, and further simultaneouslyvisualizing an outcome of said first bio-molecular modality, and anoutcome of said second clinical modality, wherein an internal database(IDB) comprises a collection of data, the analysis results, flowdefinitions, and tool definitions, and other related data for tools thatutilize a database repository, wherein a database access unit (DA)provides access to the internal database, and wherein one or moreassociated external databases (EDB) represents data stored in the systemitself, or in a database different from the internal database (IDB). 20.A memory of a computer arrangement loaded with a computer programproduct comprising instructions for performing a pre-clinical and/orclinical analysis of data obtained from at least one patient, thecomputer arrangement comprising a processing unit and the memory,wherein the computer program product when executed by the processingunit causes the processing unit to: execute, with a flow definition unit(FD), a configurable flow of analysis and visualization of a pluralityof data modalities, the plurality of data modalities comprising: a firstbio-molecular modality comprising bio-molecular data related to thepatient, and a second clinical modality comprising clinical data relatedto the patient, instantiate, with a tool execution engine (TEE), one ormore tools working on one or more of the data modalities, wherein theTEE has an interface fir the system to configure, wherein a toolrepository comprises a collection of tools for which the system isconfigured to execute, and the tools comply with a set of rules tovisualize their execution in a graphical user interface (GUI),simultaneously visualize, with the GUI, data, analysis results, and anoutcome of one or more tool executions, and further simultaneouslyvisualize an outcome of said first bio-molecular modality, and anoutcome of said second clinical modality, wherein an internal database(IDB) comprises a collection of data, the analysis results, flowdefinitions, and tool definitions, and other related data for tools thatutilize a database repository, wherein a database access unit (DA)provides access to the internal database, and wherein one or moreassociated external databases (EDB) represents data stored in the systemitself, or in a database different from the internal database (IDB).